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b.  Set a reference point (any point in between your top and bottom) 
c.  Set the top by either engaging the stepper motor and focusing up or 

entering in a number. 

d.  Set the bottom same as the top. 
e.  Set step size (the N button sets Nyquist-Shannon Sampling which is 2.7 

times the theoretical resolution limit) 

f.  Now click the green check box in the top window so when you click single 

it takes the whole z-stack (if you do this beforehand it will take a z-stack 
while you are trying to set the z-stack up) 

i.  Always make sure that the stepper motor is engaged! 

10. Zoom: 

a.  Click on the top right box with the cube in it 
b.  Use this corners of the box to zoom in and grab the middle to move it 

around 

c.  To zoom out drag the field zoom bar in the XY window all the way to the 

right 

d.  Check the XY tab to see what your pizel size is and whether you are 

doing Nyquist-Shannon Sampling (2.7 times the resolution limit).  You 
know you have reached this because the note ‘not optimum pixel size’ 
disappears. 

11. XY basic: 

a.  Pixel dwell time: this is how long the laser stays on one pixel.  I usually 

leave this at the minimum time. 

b.  Field zoom: the zooming that you have done in step 10. 
c.  Pixels: I recommend using either 512x512 or 1024x1024 but you can do 

arbitrary if you want 

12. Time: 

a.  Use this to set up your time-series: interval and number of acquisitions. 

 

 
 

Notes: 

1.  Saving Files: 

a.  Always save them as .ids (this will save 2 files: a .ids and .ics and both of 

them are needed to open it at a later date) 

2.  Spectral Un-mixing:  (only for when using the spectral detector) 

a.  Draw a ROI on image on each single color that you want to unmix (just 

red or just green – it can be useful to have samples that are only stained 
with one color for this) 

b.  Menu: Spectral

Unmix

follow script. 

3.  3 Dimensional Rendering: 

a.  Data

Volume

Volume Render 

4.  3D Orthogonal Rendering: (my favorite way to image a z-stack in EZ-C1) 

a.  Go to view and then in the drop down menu select 3D Orthogonal 

i.  This allows you to image XY, XZ, and YZ at the same time 

 

Summary of Contents for C1si

Page 1: ...Microscope User Guide Contents C1Si Turn On ShutDown Procedures 2 Overview 4 Setup for epi illumination to view through the eyepieces 5 Setup for confocal imaging 5 Notes 6 Troubleshooting 7 Owners Consortium Department of Pathology SABRE Proctor Foundation ...

Page 2: ...the up position Use both hands and gently thread it until it is finger tight Do not over tighten it or it will get stuck Available Objectives Dipping objectives are designed to form an image without a cover slip whereas immersion lenses require a cover slip For ideal imaging always use 1 5 cover slips You can then switch between the two different objectives that you have loaded by turning the leve...

Page 3: ...ou need to push the eyepiece slider in open the shutter and choose the GFP filter cube it gets very bright so you can put in the neutral density filters on the back right of the scope so you don t blind yourself b Engage the confocal pull eyepiece slider out close shutter and move filter cube to open position 6 c Turn the software onto live and set it up so the color changes with intensity 256x256...

Page 4: ...It has 2 types of detectors one with 3 standard band pass detectors and one with a spectral detector that can image 32 different channels at the same time they can be set to be 2 5nm 5nm and 10nm wide It is on an upright Nikon FN1 microscope with a large electrophysiology stage The max penetration depth into tissue is approximately 100 200 µm depending on the opacity of the sample To move the obje...

Page 5: ...ckground is black a If you are using frame lambda set up each pass individually b Set your pinhole generally it is best to leave it at a small 30 micron pinhole unless there is a compelling reason to change it 6 If using the standard detector set the detector gains at 6 5 your usable range is generally between 5 and 8 7 Go live and slowly turn up the laser power to your sample and then increase de...

Page 6: ...olution limit You know you have reached this because the note not optimum pixel size disappears 11 XY basic a Pixel dwell time this is how long the laser stays on one pixel I usually leave this at the minimum time b Field zoom the zooming that you have done in step 10 c Pixels I recommend using either 512x512 or 1024x1024 but you can do arbitrary if you want 12 Time a Use this to set up your time ...

Page 7: ...s set to 6 The eyepiece scanhead changer is pulled out Both the detector and laser are turned on so they are colored The detectors that you want are moved to 6 5 or higher The sliders for the Lasers that you want are on Your sample is getting photo bleached too quickly Try using less laser power and more detector gain Try focusing using single frames instead of live Your image is too noisy Try inc...

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